--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scHicPlotClusterProfiles.xml	Thu Jan 23 20:54:33 2020 +0000
@@ -0,0 +1,102 @@
+<tool id="schicexplorer_schicplotclusterprofiles" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>plot single-cell Hi-C interaction matrices cluster profiles</description>
+    <macros>
+        <token name="@BINARY@">scHicPlotClusterProfiles</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @BINARY@
+
+        --matrix $matrix_mcooler
+        --clusters $clusters
+        #if $chromosomes:
+            #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
+            --chromosomes $chromosome
+        #end if
+        
+        #if $order_by_conditional.order_by_selection == 'orderByFile':
+            --orderBy $order_by_conditional.order_by_selection
+        #elif $order_by_conditional.order_by_selection == 'svl':
+            --orderBy $order_by_conditional.order_by_selection
+            --distanceShortRange $order_by_conditional.distanceShortRange
+            --distanceLongRange $order_by_conditional.distanceLongRange
+        #end if
+        #if $dpi:
+            --dpi $dpi
+        #end if 
+        --outFileName plot.$image_file_format
+
+        --threads @THREADS@
+
+        && mv plot.$image_file_format plot
+
+    ]]></command>
+    <inputs>
+        <expand macro="matrix_mcooler_macro"/>
+        <param name='clusters' type='data' format='txt' label='Cluster file' help='Cluster file created by scHicCluster, scHicClusterCompartments, scHicClusterMinHash or scHicClusterSVL'/>
+        <param name="maximalDistance" type="integer" value="2000000"  label="Maximal distance" help='Maximal distance to consider for plotting' />   
+        <conditional name="order_by_conditional">
+            <param name='order_by_selection' label='Order samples by' type='select'>
+                <option value='svl' selected='true'>Short vs long range ratio</option>
+                <option value='orderByFile'>Order by file</option>
+            </param>
+            <when value='svl' >
+                <param name="distanceShortRange" type="integer" value="2000000"  label="Distance short range" help='Distance for the short range to compute the ratio of sum (short range interactions) / sum (long range interactions)' />   
+                <param name="distanceLongRange" type="integer" value="12000000"  label="Distance long range" help='Distance for the long range to compute the ratio of sum (short range interactions) / sum (long range interactions)' />   
+            </when>
+            <when value='orderByFile'>
+            </when>
+        </conditional>
+        <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
+        <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
+        
+        <param name="image_file_format" type="select" label="Image output format">
+            <option value="png" selected="True">png</option>
+            <option value="svg">svg</option>
+            <option value="pdf">pdf</option>
+        </param>
+        
+    </inputs>
+    <outputs>
+        <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
+            <change_format>
+                <when input="image_file_format" value="svg" format="svg" />
+                <when input="image_file_format" value="pdf" format="pdf" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='clusters' value='scHicPlotClusterProfiles/cluster_kmeans.txt' />
+            <conditional name="order_by_conditional">
+                <param name="order_by_selection" value="svl"/>
+                <param name="distanceShortRange" value="2000000" />
+                <param name="distanceLongRange" value="12000000" />
+            </conditional>
+            <param name="maximalDistance" value="50000000" />
+            <param name="image_file_format" value="png" />
+            <param name="dpi" value="300" />
+
+            <output name="output_plot" file="scHicPlotClusterProfiles/plot.png" ftype="png" compare="sim_size" delta="35000"/>        
+        </test>
+       
+    </tests>
+    <help><![CDATA[
+
+Plot cluster profiles
+=====================
+
+scHicPlotClusterProfiles plots the profile of each scHi-C interaction matrix assoziated to a cluster, within the cluster the matrices can be order either via their short vs long range ratio or by the order of the file.
+
+.. image:: $PATH_TO_IMAGES/clusters_svl_spectral.png
+   :width: 50%
+
+For more information about scHiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://schicexplorer.readthedocs.io/
+]]></help>
+    <expand macro="citations" />
+
+</tool>
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